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| source("utils.R") | |
| source("inat-ranges.R") | |
| url <- "https://s3-west.nrp-nautilus.io/public-data/cache/inat/f0108ef86feababffeab3d2be6f09373.h3j" | |
| #url <- "https://minio.carlboettiger.info/public-data/cache/inat/4fd3323845ee860b39609783566b2212.h3j" | |
| url <- "https://minio.carlboettiger.info/public-data/cache/inat/f0108ef86feababffeab3d2be6f09373.h3j" | |
| #x <- jsonlite::read_json(url) | |
| m = maplibre(center = c(-110,37), zoom=3) |> | |
| add_draw_control() |> | |
| add_h3j_source("h3j_source", | |
| url = url | |
| ) |> | |
| add_fill_extrusion_layer( | |
| id = "h3j_layer", | |
| source = "h3j_source", | |
| tooltip = "n", | |
| fill_extrusion_color = viridis_pal("height"), | |
| fill_extrusion_height = list( | |
| "interpolate", | |
| list("linear"), | |
| list("zoom"), | |
| 0, | |
| 0, 1, | |
| list("*", 100000, list("get", "height")) | |
| ), | |
| fill_extrusion_opacity = 0.7 | |
| ) | |
| htmlwidgets::saveWidget(m, "test2.html") | |
| ## Illustrate/test core app functionality without shiny | |
| library(dplyr) | |
| library(duckdbfs) | |
| library(ggplot2) | |
| library(mapgl) | |
| library(glue) | |
| library(jsonlite) | |
| load_h3() | |
| load_spatial() | |
| source("utils.R") | |
| source("inat-ranges.R") | |
| duckdbfs::duckdb_secrets() | |
| inat <- open_dataset("s3://public-inat/hex") | |
| aoi <- spData::us_states | |
| aoi <- spData::world | |
| # publish richness at the aoi (bbox or poly) | |
| meta <- richness(inat, aoi) | |
| m <- richness_map(meta) | |
| m | |
| library(htmlwidgets) | |
| htmlwidgets::saveWidget(m, "total-richness.html") | |
| # publish richness at the aoi (bbox or poly) | |
| meta <- richness(inat, aoi, rank = "class", taxon = "Aves") | |
| m <- richness_map(meta) | |
| htmlwidgets::saveWidget(m, "aves-richness.html") | |
| # publish richness at the aoi (bbox or poly) | |
| meta <- richness(inat, aoi, rank = "class", taxon = "Mammalia") | |
| m <- richness_map(meta) | |
| htmlwidgets::saveWidget(m, "mammals-richness.html") | |
| ## UGH can't deal with antimeridian | |
| # dropme <- antimeridian_hexes(3) | |
| # dropme <- antimeridian_hexes(4) |> rename(h4 = h3id) | |
| # inat |> anti_join(dropme) |> write_dataset("s3://public-inat/ranges.parquet") | |
| # inat <- open_dataset("s3://public-inat/ranges.parquet", recursive = FALSE) | |
| # mutate(h3 = h3_cell_to_parent(h4, 3L)) | |
| m <- maplibre(center = c(-110.5, 34.8), zoom = 4) |> add_draw_control() | |
| richness_map(m, "https://minio.carlboettiger.info/public-data/inat-tmp-ranges.h3j") | |
| library(htmlwidgets) | |
| htmlwidgets::saveWidget(m, "example.html") | |
| amphib = open_dataset("s3://public-inat/polygon/Amphibia.parquet", recursive = FALSE) | |
| gdf <- amphib |> | |
| filter(name == "Ambystoma californiense") |> | |
| to_sf(crs=4326) | |
| maplibre(center = c(-122.5, 37.8), zoom = 4) |> | |
| add_source(id = "gdf", gdf) |> | |
| add_layer("gdf-layer", | |
| type = "fill", | |
| source = "gdf", | |
| paint = list( | |
| "fill-color" = "darkgreen", | |
| "fill-opacity" = .9 | |
| ) | |
| ) | |
| # Access SVI | |
| #svi = open_dataset("https://minio.carlboettiger.info/public-social-vulnerability/2022/SVI2022_US_tract.parquet") | |
| #tracts = open_dataset("https://minio.carlboettiger.info/public-social-vulnerability/2022-tracts-h3-z5.parquet") # Access CalEnviroScreen | |
| # ces = open_dataset("https://minio.carlboettiger.info/public-calenviroscreen/ces_2021.parquet", format="parquet") | |
| # Filter GBIF to our area-of-interest (h-index) and species of interest | |
| ca <- tracts |> | |
| filter(STATE == "California") |> | |
| mutate(h4 = h3_cell_to_parent(h5, 4L)) |> | |
| mutate(h4 = tolower(as.character(h4))) | |
| out <- ca |> | |
| inner_join(inat, by = "h4") |> | |
| count(STATE, COUNTY, FIPS, h5) | |
| # mutate(height = n / max(n)) |> | |
| url = "https://minio.carlboettiger.info/public-data/cache/inat/cec4b3087f0b6c41ecc384da2521f97c.h3j" | |
| maplibre() |> | |
| add_draw_control() |> | |
| add_h3j_source("h3j_source", | |
| url = url | |
| ) |> | |
| add_fill_extrusion_layer( | |
| id = "h3j_layer", | |
| source = "h3j_source", | |
| tooltip = "n", | |
| fill_extrusion_color = viridis_pal("height"), | |
| fill_extrusion_height = list( | |
| "interpolate", | |
| list("linear"), | |
| list("zoom"), | |
| 0, | |
| 0, 1, | |
| list("*", 100000, list("get", "height")) | |
| ), | |
| fill_extrusion_opacity = 0.7 | |
| ) | |